Research Insights

Even in fungal model systems, up to 40% of genes have unknown or poorly characterized functions with no informative homologies in databases. Fungi tolerate a variety of stressful environments, including a wide range of temperature and moisture levels. The same fungal species isolated from different environments often shows variation in its genetic complement. Studies of pan-genomes (the full genetic complement of a species assembled from varied individuals) have identified core genes (present in all isolates), accessory genes (present in >1 isolate) and singleton genes (present in only 1 isolate). Accessory and singleton genes are much more likely to have an unknown or poorly characterized function, presumably because these genes have evolved or been retained only in a subset of environments.

We propose to exploit natural variation in two fungal species to identify genes of unknown function that allow them to survive across temperature and moisture ranges. We have previously collected isolates of the filamentous fungus Aspergillus fumigatus and the yeast Saccharomyces paradoxus from a range of urban, natural, and agricultural environments in North America. Our collection sites spanned a wide range of temperature and moisture levels, and we already have WGS data for many of the isolates.

We propose to construct pan-genomes for A. fumigatus and S. paradoxus and identify core, accessory, and singleton genes and genes of unknown or poorly characterized function. We will pick environmental isolates of A. fumigatus and S. paradoxus representing the environments with the most extreme temperatures (coldest and warmest) and humidity (driest and wettest) that also have the most genes of unknown or poorly characterized function. Transcriptomes will be analyzed from these strains grown under a variety of temperature and humidity levels. We will identify genes that are differentially expressed across conditions, especially those with unknown or poorly defined functions. We will create gene deletions and tags and use them in functional validation experiments for genes of unknown or poorly characterized function whose expression suggests roles in response to temperature and/or humidity variation.

Our ultimate goals are to reduce the number of genes of unknown/poorly characterized function in the filamentous fungus A. fumigatus and the yeast S. paradoxus and to discover new genes that are important for tolerance to a range of temperature and water-availability levels in these fungi. If this approach proves successful, it can be used for gene discovery in other fungi, including nonmodel systems that lack genetic tools and will allow improved prediction of the resilience of other species of environmental fungi. Though it is currently appreciated that there is environmental variation in species, this variation has not been used in the way we propose to assign gene function. Thus, the proposed experiments will serve as a guide for future work leveraging natural variation and phenotyping to assign function to fungal genes of unknown function, especially those that allow fungi to thrive in hostile environments. Understanding such genes will be helpful to the Army because fungi are notorious for degrading materials in the challenging environments where the Army’s missions often occur.

Funder: U.S. Department of the Army

Amount: $449,999

PI: Michelle Momany, Franklin College of Arts and Sciences, Department of Plant Biology